[2023-03-16 04:54:07,040] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference
[2023-03-16 04:54:08,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,356] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,356] [INFO] Running command: cat /var/lib/cwl/stg8adc2c34-b3c4-466d-ad26-4185de9079ee/OceanDNA-a2388.fa | prodigal -d OceanDNA-a2388/cds.fna -a OceanDNA-a2388/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:17,494] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:17,494] [INFO] Task started: HMMsearch
[2023-03-16 04:54:17,494] [INFO] Running command: hmmsearch --tblout OceanDNA-a2388/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/reference_markers.hmm OceanDNA-a2388/protein.faa > /dev/null
[2023-03-16 04:54:17,690] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:17,690] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8adc2c34-b3c4-466d-ad26-4185de9079ee/OceanDNA-a2388.fa]
[2023-03-16 04:54:17,703] [INFO] Query marker FASTA was written to OceanDNA-a2388/markers.fasta
[2023-03-16 04:54:17,703] [INFO] Task started: Blastn
[2023-03-16 04:54:17,703] [INFO] Running command: blastn -query OceanDNA-a2388/markers.fasta -db /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/reference_markers.fasta -out OceanDNA-a2388/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:18,131] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:18,132] [INFO] Selected 7 target genomes.
[2023-03-16 04:54:18,132] [INFO] Target genome list was writen to OceanDNA-a2388/target_genomes.txt
[2023-03-16 04:54:18,136] [INFO] Task started: fastANI
[2023-03-16 04:54:18,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg8adc2c34-b3c4-466d-ad26-4185de9079ee/OceanDNA-a2388.fa --refList OceanDNA-a2388/target_genomes.txt --output OceanDNA-a2388/fastani_result.tsv --threads 1
[2023-03-16 04:54:23,228] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:23,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:23,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:23,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:23,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:23,229] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-16 04:54:23,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2388/tc_result.tsv
[2023-03-16 04:54:23,229] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:23,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:23,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/checkm_data
[2023-03-16 04:54:23,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:23,238] [INFO] Task started: CheckM
[2023-03-16 04:54:23,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2388/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2388/checkm_input OceanDNA-a2388/checkm_result
[2023-03-16 04:54:52,047] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:52,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:54:52,050] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:52,051] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:52,051] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2388/markers.fasta)
[2023-03-16 04:54:52,051] [INFO] Task started: Blastn
[2023-03-16 04:54:52,051] [INFO] Running command: blastn -query OceanDNA-a2388/markers.fasta -db /var/lib/cwl/stg3d85e3a2-eedf-4fa6-8325-d7945e55b848/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2388/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:52,513] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:52,515] [INFO] Selected 9 target genomes.
[2023-03-16 04:54:52,515] [INFO] Target genome list was writen to OceanDNA-a2388/target_genomes_gtdb.txt
[2023-03-16 04:54:52,526] [INFO] Task started: fastANI
[2023-03-16 04:54:52,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg8adc2c34-b3c4-466d-ad26-4185de9079ee/OceanDNA-a2388.fa --refList OceanDNA-a2388/target_genomes_gtdb.txt --output OceanDNA-a2388/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:54:55,572] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:55,578] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:54:55,578] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_009937025.1	s__MGIIa-L1 sp009937025	95.5864	397	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018662825.1	s__MGIIa-L1 sp018662825	84.1864	396	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_002170315.2	s__MGIIa-L1 sp002170315	79.8902	272	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182635.1	s__MGIIa-L1 sp905182635	79.6733	233	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499705.1	s__MGIIa-L1 sp002499705	79.6189	254	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182715.1	s__MGIIa-L1 sp905182715	79.5806	244	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182725.1	s__MGIIa-L1 sp905182725	79.5146	263	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520595.1	s__MGIIa-L1 sp902520595	79.4949	159	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002506275.1	s__MGIIa-L1 sp002506275	78.089	112	471	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	-
--------------------------------------------------------------------------------
[2023-03-16 04:54:55,579] [INFO] GTDB search result was written to OceanDNA-a2388/result_gtdb.tsv
[2023-03-16 04:54:55,579] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:54:55,580] [INFO] DFAST_QC result json was written to OceanDNA-a2388/dqc_result.json
[2023-03-16 04:54:55,580] [INFO] DFAST_QC completed!
[2023-03-16 04:54:55,580] [INFO] Total running time: 0h0m49s